| 4215 |
10.1016/j.cell.2018.05.061 |
Recovering Gene Interactions From Single-Cell Data
Using Data Diffusion |
|
Cell |
2018 |
| 4220 |
10.1016/j.cell.2018.06.052 |
A Single-Cell Atlas Of In Vivo Mammalian Chromatin
Accessibility |
Cusanovich, Darren A.; Hill, Andrew J.; Aghamirzaie,
Delasa; Daza, Riza M.; Pliner, Hannah A.; Berletch, Joel B.; Filippova,
Galina N.; Huang, Xingfan; Christiansen, Lena; Dewitt, William S.; Lee,
Choli; Regalado, Samuel G.; Read, David F.; Steemers, Frank J.;
Disteche, Christine M.; Trapnell, Cole; Shendure, Jay |
Cell |
2018 |
| 4276 |
10.1016/j.cell.2019.03.014 |
Profiling Of Pluripotency Factors In Single Cells And
Early Embryos |
Hainer, Sarah J.; Bo<U+0161>kovi<U+0107>,
Ana; Mccannell, Kurtis N.; Rando, Oliver J.; Fazzio, Thomas G. |
Cell |
2019 |
| 4287 |
10.1016/j.cell.2019.05.006 |
Single-Cell Multi-Omic Integration Compares And
Contrasts Features Of Brain Cell Identity |
Welch, Joshua D.; Kozareva, Velina; Ferreira, Ashley;
Vanderburg, Charles; Martin, Carly; Macosko, Evan Z. |
Cell |
2019 |
| 4290 |
10.1016/j.cell.2019.05.031 |
Comprehensive Integration Of Single-Cell Data |
Stuart, Tim; Butler, Andrew; Hoffman, Paul;
Hafemeister, Christoph; Papalexi, Efthymia; Mauck, William M.; Hao,
Yuhan; Stoeckius, Marlon; Smibert, Peter; Satija, Rahul |
Cell |
2019 |
| 4414 |
10.1016/j.cell.2020.09.056 |
Chromatin Potential Identified By Shared Single-Cell
Profiling Of Rna And Chromatin |
Ma, Sai; Zhang, Bing; Lafave, Lindsay M.; Earl, Andrew
S.; Chiang, Zachary; Hu, Yan; Ding, Jiarui; Brack, Alison; Kartha, Vinay
K.; Tay, Tristan; Law, Travis; Lareau, Caleb; Hsu, Ya-Chieh; Regev,
Aviv; Buenrostro, Jason D. |
Cell |
2020 |
| 8195 |
10.1016/j.molcel.2018.06.044 |
Cicero Predicts Cis-Regulatory Dna Interactions From
Single-Cell Chromatin Accessibility Data |
Pliner, Hannah A.; Packer, Jonathan S.;
Mcfaline-Figueroa, Jose L.; Cusanovich, Darren A.; Daza, Riza M.;
Aghamirzaie, Delasa; Srivatsan, Sanjay; Qiu, Xiaojie; Jackson, Dana;
Minkina, Anna; Adey, Andrew C.; Steemers, Frank J.; Shendure, Jay;
Trapnell, Cole |
Molecular Cell |
2018 |
| 8236 |
10.1016/j.molcel.2019.07.015 |
Cobatch For High-Throughput Single-Cell Epigenomic
Profiling |
Wang, Qianhao; Xiong, Haiqing; Ai, Shanshan; Yu,
Xianhong; Liu, Yaxi; Zhang, Jiejie; He, Aibin |
Molecular Cell |
2019 |
| 12753 |
10.1038/s41467-018-03405-7 |
An Accurate And Robust Imputation Method Scimpute For
Single-Cell Rna-Seq Data |
Li, Wei Vivian, 0000-0002-2087-2709; Li, Jingyi
Jessica, 0000-0002-9288-5648 |
Nature Communications |
2018 |
| 12887 |
10.1038/s41467-018-07931-2 |
Single-Cell Rna-Seq Denoising Using A Deep Count
Autoencoder |
Eraslan, Gokcen, 0000-0001-9579-2909; Simon, Lukas M.,
0000-0001-6148-8861; Mircea, Maria, 0000-0002-1935-8665; Mueller, Nikola
S.; Theis, Fabian J., 0000-0002-2419-1943 |
Nature Communications |
2019 |
| 12909 |
10.1038/s41467-018-08205-7 |
Deconvolution Of Single-Cell Multi-Omics Layers Reveals
Regulatory Heterogeneity |
Liu, Longqi; Liu, Chuanyu; Quintero, Andres,
0000-0002-3959-805X; Wu, Liang; Yuan, Yue; Wang, Mingyue; Cheng,
Mengnan; Leng, Lizhi; Xu, Liqin; Dong, Guoyi; Li, Rui; Liu, Yang; Wei,
Xiaoyu; Xu, Jiangshan; Chen, Xiaowei; Lu, Haorong; Chen, Dongsheng;
Wang, Quanlei; Zhou, Qing; Lin, Xinxin; Li, Guibo, 0000-0002-6141-4931;
Liu, Shiping, 0000-0003-0019-619X; Wang, Qi; Wang, Hongru; Fink, J.
Lynn; Gao, Zhengliang; Liu, Xin, 0000-0003-3256-2940; Hou, Yong,
0000-0002-0420-0726; Zhu, Shida; Yang, Huanming; Ye, Yunming; Lin, Ge;
Chen, Fang; Herrmann, Carl; Eils, Roland, 0000-0002-0034-4036; Shang,
Zhouchun, 0000-0002-1740-7961; Xu, Xun |
Nature Communications |
2019 |
| 13051 |
10.1038/s41467-019-09982-5 |
Cut&Tag For Efficient Epigenomic Profiling Of Small
Samples And Single Cells |
Kaya-Okur, Hatice S.; Wu, Steven J.; Codomo, Christine
A.; Pledger, Erica S.; Bryson, Terri D.; Henikoff, Jorja G.; Ahmad,
Kami, 0000-0001-8572-6182; Henikoff, Steven |
Nature Communications |
2019 |
| 13130 |
10.1038/s41467-019-11559-1 |
Mapping Histone Modifications In Low Cell Number And
Single Cells Using Antibody-Guided Chromatin Tagmentation (Act-Seq) |
Carter, Benjamin, 0000-0001-6530-9568; Ku, Wai Lim,
0000-0002-8859-6771; Kang, Jee Youn; Hu, Gangqing; Perrie, Jonathan;
Tang, Qingsong; Zhao, Keji, 0000-0001-5559-6233 |
Nature Communications |
2019 |
| 13175 |
10.1038/s41467-019-12630-7 |
Scale Method For Single-Cell Atac-Seq Analysis Via
Latent Feature Extraction |
Xiong, Lei, 0000-0002-2392-114X; Xu, Kui; Tian, Kang;
Shao, Yanqiu; Tang, Lei; Gao, Ge; Zhang, Michael; Jiang, Tao,
0000-0003-3833-4498; Zhang, Qiangfeng Cliff, 0000-0002-4913-0338 |
Nature Communications |
2019 |
| 13474 |
10.1038/s41556-018-0248-3 |
A Chromatin Integration Labelling Method Enables
Epigenomic Profiling With Lower Input |
Harada, Akihito; Maehara, Kazumitsu; Handa, Tetsuya;
Arimura, Yasuhiro; Nogami, Jumpei; Hayashi-Takanaka, Yoko; Shirahige,
Katsuhiko; Kurumizaka, Hitoshi; Kimura, Hiroshi, 0000-0003-0854-083X;
Ohkawa, Yasuyuki, 0000-0001-6440-9954 |
Nature Cell Biology |
2018 |
| 13484 |
10.1038/s41556-019-0383-5 |
Profiling Chromatin States Using Single-Cell
Itchip-Seq |
Ai, Shanshan; Xiong, Haiqing; Li, Chen C.; Luo,
Yingjie; Shi, Qiang; Liu, Yaxi; Yu, Xianhong; Li, Cheng; He, Aibin,
0000-0002-3489-2305 |
Nature Cell Biology |
2019 |
| 14503 |
10.1038/s41587-019-0113-3 |
Efficient Integration Of Heterogeneous Single-Cell
Transcriptomes Using Scanorama |
Hie, Brian, 0000-0003-3224-8142; Bryson, Bryan,
0000-0003-1716-6712; Berger, Bonnie, 0000-0002-2724-7228 |
Nature Biotechnology |
2019 |
| 14505 |
10.1038/s41587-019-0147-6 |
Droplet-Based Combinatorial Indexing For Massive-Scale
Single-Cell Chromatin Accessibility |
Lareau, Caleb A., 0000-0003-4179-4807; Duarte, Fabiana
M., 0000-0002-1261-4929; Chew, Jennifer G.; Kartha, Vinay K.,
0000-0002-2160-2196; Burkett, Zach D., 0000-0002-5153-485X; Kohlway,
Andrew S.; Pokholok, Dmitry; Aryee, Martin J., 0000-0002-6848-1344;
Steemers, Frank J.; Lebofsky, Ronald, 0000-0002-3728-6415; Buenrostro,
Jason D., 0000-0001-9958-3987 |
Nature Biotechnology |
2019 |
| 14508 |
10.1038/s41587-019-0206-z |
Massively Parallel Single-Cell Chromatin Landscapes Of
Human Immune Cell Development And Intratumoral T Cell Exhaustion |
Satpathy, Ansuman T., 0000-0002-5167-537X; Granja,
Jeffrey M.; Yost, Kathryn E.; Qi, Yanyan; Meschi, Francesca; Mcdermott,
Geoffrey P.; Olsen, Brett N.; Mumbach, Maxwell R.; Pierce, Sarah E.,
0000-0002-9145-9559; Corces, M. Ryan; Shah, Preyas; Bell, Jason C.;
Jhutty, Darisha; Nemec, Corey M.; Wang, Jean; Wang, Li; Yin, Yifeng;
Giresi, Paul G.; Chang, Anne Lynn S., 0000-0002-2869-2147; Zheng, Grace
X. Y., 0000-0002-5006-3785; Greenleaf, William J., 0000-0003-1409-3095;
Chang, Howard Y., 0000-0002-9459-4393 |
Nature Biotechnology |
2019 |
| 14520 |
10.1038/s41587-019-0290-0 |
High-Throughput Sequencing Of The Transcriptome And
Chromatin Accessibility In The Same Cell |
Chen, Song, 0000-0001-5286-3084; Lake, Blue B.,
0000-0002-8637-9044; Zhang, Kun, 0000-0002-7596-5224 |
Nature Biotechnology |
2019 |
| 14523 |
10.1038/s41587-019-0332-7 |
Single-Cell Multiomic Analysis Identifies Regulatory
Programs In Mixed-Phenotype Acute Leukemia |
Granja, Jeffrey M.; Klemm, Sandy, 0000-0001-7556-6795;
Mcginnis, Lisa M.; Kathiria, Arwa S.; Mezger, Anja; Corces, M. Ryan;
Parks, Benjamin, 0000-0002-0261-7472; Gars, Eric; Liedtke, Michaela;
Zheng, Grace X. Y., 0000-0002-5006-3785; Chang, Howard Y.,
0000-0002-9459-4393; Majeti, Ravindra; Greenleaf, William J.,
0000-0003-1409-3095 |
Nature Biotechnology |
2019 |
| 14578 |
10.1038/s41588-019-0424-9 |
High-Throughput Single-Cell Chip-Seq Identifies
Heterogeneity Of Chromatin States In Breast Cancer |
Grosselin, Kevin, 0000-0001-6189-3197; Durand, Adeline,
0000-0002-7423-2504; Marsolier, Justine; Poitou, Adeline; Marangoni,
Elisabetta; Nemati, Fariba; Dahmani, Ahmed; Lameiras, Sonia; Reyal,
Fabien; Frenoy, Olivia; Pousse, Yannick; Reichen, Marcel; Woolfe, Adam;
Brenan, Colin; Griffiths, Andrew D., 0000-0002-0808-3539; Vallot,
Celine, 0000-0003-1601-2359; Gerard, Annabelle, 0000-0003-0411-768X |
Nature Genetics |
2019 |
| 14761 |
10.1038/s41592-018-0033-z |
Saver: Gene Expression Recovery For Single-Cell Rna
Sequencing |
Huang, Mo; Wang, Jingshu; Torre, Eduardo; Dueck,
Hannah; Shaffer, Sydney; Bonasio, Roberto; Murray, John I.; Raj, Arjun;
Li, Mingyao; Zhang, Nancy R. |
Nature Methods |
2018 |
| 14768 |
10.1038/s41592-018-0229-2 |
Deep Generative Modeling For Single-Cell
Transcriptomics |
Lopez, Romain; Regier, Jeffrey, 0000-0002-1472-5235;
Cole, Michael B.; Jordan, Michael I.; Yosef, Nir,
0000-0001-9004-1225 |
Nature Methods |
2018 |
| 14771 |
10.1038/s41592-018-0254-1 |
A Test Metric For Assessing Single-Cell Rna-Seq Batch
Correction |
Buttner, Maren, 0000-0002-6189-3792; Miao, Zhichao;
Wolf, F. Alexander, 0000-0002-8760-7838; Teichmann, Sarah A.,
0000-0002-6294-6366; Theis, Fabian J., 0000-0002-2419-1943 |
Nature Methods |
2018 |
| 14776 |
10.1038/s41592-019-0353-7 |
Scalable Analysis Of Cell-Type Composition From
Single-Cell Transcriptomics Using Deep Recurrent Learning |
Deng, Yue; Bao, Feng; Dai, Qionghai; Wu, Lani F.,
0000-0002-0052-7537; Altschuler, Steven J., 0000-0001-9142-0796 |
Nature Methods |
2019 |
| 14777 |
10.1038/s41592-019-0361-7 |
Single-Cell Chromatin Immunocleavage Sequencing
(Scchic-Seq) To Profile Histone Modification |
Ku, Wai Lim; Nakamura, Kosuke; Gao, Weiwu; Cui,
Kairong; Hu, Gangqing; Tang, Qingsong; Ni, Bing, 0000-0002-4297-5346;
Zhao, Keji, 0000-0001-5559-6233 |
Nature Methods |
2019 |
| 14778 |
10.1038/s41592-019-0367-1 |
Cistopic: Cis-Regulatory Topic Modeling On Single-Cell
Atac-Seq Data |
Bravo Gonzalez-Blas, Carmen, 0000-0003-0973-9410;
Minnoye, Liesbeth, 0000-0002-0898-2817; Papasokrati, Dafni,
0000-0002-1524-2155; Aibar, Sara, 0000-0001-6104-7134; Hulselmans, Gert,
0000-0003-2205-1899; Christiaens, Valerie; Davie, Kristofer,
0000-0003-2182-1249; Wouters, Jasper, 0000-0002-7129-2990; Aerts, Stein,
0000-0002-8006-0315 |
Nature Methods |
2019 |
| 14787 |
10.1038/s41592-019-0466-z |
Joint Analysis Of Heterogeneous Single-Cell Rna-Seq
Dataset Collections |
Barkas, Nikolas, 0000-0002-4675-0718; Petukhov, Viktor;
Nikolaeva, Daria; Lozinsky, Yaroslav; Demharter, Samuel; Khodosevich,
Konstantin; Kharchenko, Peter V., 0000-0002-6036-5875 |
Nature Methods |
2019 |
| 14790 |
10.1038/s41592-019-0494-8 |
Scgen Predicts Single-Cell Perturbation Responses |
Lotfollahi, Mohammad, 0000-0001-6858-7985; Wolf, F.
Alexander, 0000-0002-8760-7838; Theis, Fabian J.,
0000-0002-2419-1943 |
Nature Methods |
2019 |
| 14793 |
10.1038/s41592-019-0537-1 |
Data Denoising With Transfer Learning In Single-Cell
Transcriptomics |
Wang, Jingshu; Agarwal, Divyansh, 0000-0003-0404-6877;
Huang, Mo, 0000-0002-8399-7525; Hu, Gang; Zhou, Zilu; Ye, Chengzhong;
Zhang, Nancy R., 0000-0002-0880-5749 |
Nature Methods |
2019 |
| 14797 |
10.1038/s41592-019-0576-7 |
Exploring Single-Cell Data With Deep Multitasking
Neural Networks |
Amodio, Matthew; Van Dijk, David; Srinivasan, Krishnan;
Chen, William S.; Mohsen, Hussein, 0000-0002-6263-8865; Moon, Kevin R.;
Campbell, Allison; Zhao, Yujiao; Wang, Xiaomei; Venkataswamy,
Manjunatha; Desai, Anita; Ravi, V.; Kumar, Priti; Montgomery, Ruth,
0000-0002-8661-4454; Wolf, Guy, 0000-0002-6740-059X; Krishnaswamy,
Smita, 0000-0001-5823-1985 |
Nature Methods |
2019 |
| 14803 |
10.1038/s41592-019-0619-0 |
Fast, Sensitive And Accurate Integration Of Single-Cell
Data With Harmony |
Korsunsky, Ilya, 0000-0003-4848-3948; Millard, Nghia;
Fan, Jean, 0000-0002-0212-5451; Slowikowski, Kamil; Zhang, Fan,
0000-0002-6102-2970; Wei, Kevin; Baglaenko, Yuriy, 0000-0002-9020-6824;
Brenner, Michael; Loh, Po-Ru, 0000-0001-5542-9064; Raychaudhuri, Soumya,
0000-0002-1901-8265 |
Nature Methods |
2019 |
| 14807 |
10.1038/s41592-019-0691-5 |
Single-Cell Multimodal Omics: The Power Of Many |
Zhu, Chenxu; Preissl, Sebastian; Ren, Bing |
Nature Methods |
2020 |
| 14808 |
10.1038/s41592-019-0692-4 |
Computational Methods For Single-Cell Omics Across
Modalities |
Efremova, Mirjana; Teichmann, Sarah A.,
0000-0002-6294-6366 |
Nature Methods |
2020 |
| 14871 |
10.1038/s41594-019-0323-x |
An Ultra High-Throughput Method For Single-Cell Joint
Analysis Of Open Chromatin And Transcriptome |
Zhu, Chenxu, 0000-0003-4216-6562; Yu, Miao; Huang, Hui;
Juric, Ivan; Abnousi, Armen, 0000-0003-1822-0928; Hu, Rong; Lucero,
Jacinta; Behrens, M. Margarita; Hu, Ming; Ren, Bing,
0000-0002-5435-1127 |
Nature Structural & Molecular Biology |
2019 |
| 15050 |
10.1038/s42256-019-0037-0 |
Clustering Single-Cell Rna-Seq Data With A Model-Based
Deep Learning Approach |
Tian, Tian, 0000-0001-6147-1082; Wan, Ji; Song, Qi;
Wei, Zhi, 0000-0001-6059-4267 |
Nature Machine Intelligence |
2019 |
| 16407 |
10.1073/pnas.1820006116 |
Scmerge Leverages Factor Analysis, Stable Expression,
And Pseudoreplication To Merge Multiple Single-Cell Rna-Seq
Datasets |
Lin, Yingxin; Ghazanfar, Shila; Wang, Kevin Y. X.;
Gagnon-Bartsch, Johann A.; Lo, Kitty K.; Su, Xianbin; Han, Ze-Guang;
Ormerod, John T.; Speed, Terence P.; Yang, Pengyi, 0000-0003-1098-3138;
Yang, Jean Yee Hwa, 0000-0002-5271-2603 |
Proceedings Of The National Academy Of Sciences |
2019 |
| 17019 |
10.1093/bioinformatics/btz625 |
Bbknn: Fast Batch Alignment Of Single Cell
Transcriptomes |
Pola<U+0144>ski, Krzysztof; Young, Matthew D;
Miao, Zhichao; Meyer, Kerstin B; Teichmann, Sarah A; Park, Jong-Eun |
Bioinformatics |
2019 |
| 18806 |
10.1126/science.aau0730 |
Joint Profiling Of Chromatin Accessibility And Gene
Expression In Thousands Of Single Cells |
Cao, Junyue, 0000-0003-4097-489X; Cusanovich, Darren
A., 0000-0001-6889-0095; Ramani, Vijay, 0000-0003-3345-5960;
Aghamirzaie, Delasa; Pliner, Hannah A., 0000-0003-1484-6501; Hill,
Andrew J.; Daza, Riza M., 0000-0003-1635-8675; Mcfaline-Figueroa, Jose
L., 0000-0003-4387-1511; Packer, Jonathan S., 0000-0003-4025-0007;
Christiansen, Lena, 0000-0003-1386-4871; Steemers, Frank J.; Adey,
Andrew C., 0000-0001-7648-8717; Trapnell, Cole, 0000-0002-8105-4347;
Shendure, Jay, 0000-0002-1516-1865 |
Science |
2018 |
| 20005 |
10.1186/s12859-018-2226-y |
Drimpute: Imputing Dropout Events In Single Cell Rna
Sequencing Data |
Gong, Wuming; Kwak, Il-Youp; Pota, Pruthvi;
Koyano-Nakagawa, Naoko; Garry, Daniel J. |
Bmc Bioinformatics |
2018 |